Numerous pathogens (e.g., viruses, bacteria, fungi, and parasites) cause infection and other illness in animal and human populations worldwide. Sometimes one or more mutations in a pathogen can cause a typical illness-causing pathogen to become a full-blown pandemic. Although these pathogens and resultant illnesses are varied, one of the more prominent based on current events is the influenza virus.
The influenza virus and its variations (collectively referred to herein as “the flu virus”) are the cause for a contagious respiratory illness (commonly referred to as “influenza,” “illness,” or the “Flu”) in humans and animals (interchangeably referred to herein as a “host,” “patient,” or “subject”) that can cause mild to severe illness, and at times can lead to death. Every year in the United States alone, on average: 5% to 20% of the population gets the Flu; more than 200,000 people are hospitalized from Flu complications—and about 36,000 people die from Flu.
The flu virus spreads in respiratory droplets typically transmitted through coughing and sneezing. In human patients, the virus usually spreads from person to person, though sometimes subjects become infected by touching something with flu viruses on it and then touching their mouth or nose. Most healthy adults may be able to infect others beginning 1 day before symptoms develop and up to 5 days after becoming sick. Uncomplicated influenza illness is often characterized by an abrupt onset of constitutional and respiratory signs and symptoms, including fever, myalgia, headache, malaise, nonproductive cough, sore throat, and rhinitis.
There are three main types of influenza viruses: influenza A, influenza B, and influenza C. Within each type of influenza and within influenza A in particular there are many different subtypes. These subtypes differ based upon certain proteins expressed on the surface of the virus, specifically the hemagglutinin (HA) and the neuraminidase (NA) proteins. To date sixteen HA subtypes and nine NA subtypes of influenza A virus have been reported from avian isolates. Many different combinations of HA and NA proteins are possible, however, and each combination represents a unique subtype.
“Human influenza virus” usually refers to those subtypes that spread widely among humans. There are three known influenza A subtypes currently circulating among humans: H1N1, H1N2, and H3N2, each of which include various individual influenza viral strains. Subtype H2N2, for example, (which includes strains often referred as ‘Asian Flu’ strains), circulated within the human population from 1957-1968. Subtype H1N1, which includes strains commonly referred to as ‘Swine Flu’ strains, is currently circulating within various human populations worldwide.
Alarmingly, because influenza A viruses can constantly undergo mutations, reassortments, genetic “drift and shift,” and the like, host specificities are changing. Influenza viruses can be spread among various animal species, and infection from non-human species (such as avians, porcines, primates, and other animals) to human hosts leads to new influenza subtypes that can adapt over time to infect and spread more rapidly or thoroughly among human populations. Examples that have been widely reported in recent years include, for example, H5, H7, and H9 subtypes.
The H5N1 subtype, for example, has been reported as having mutated sufficiently to spread from avian hosts to humans. While the spread of H5N1 virus from human to human has, at least for now, been limited, unfortunately that has not been the case with the spread of particular strains of the H1N1 subtype, which appear to be highly contagious, and infectious when spread from person to person. Additionally, because H5N1, H1N1, and many other subtypes have been historically less prevalent in human populations, there is little or no immune protection against them in humans at present. Indeed, it has been widely reported in the mainstream media, and commonly considered in the scientific community that, if virulent strains of Influenza A virus were to gain the capacity to spread easily from person to person, a worldwide outbreak of disease (i.e., pandemic) would likely ensue. The mid-summer 2009 declaration by the World Health Organization (WHO) that the spread of H1N1 influenza had reached Phase 6 pandemic proportion (nearly 100,000 laboratory-confirmed cases and over 400 deaths) in more than 120 countries, confirms this conventional wisdom.
Pandemic viruses typically emerge as a result of a process called “antigenic shift,” which causes an abrupt or sudden, major change in a virus, e.g., influenza A virus. In the process of antigenic shift, two or more different strains of a single virus (or of different viruses), combine to form a distinctly new subtype that expresses a unique combination of surface antigens found in the strains that originally combined. While antigenic shift has been reported in various viral species, it is most widely observed in influenza virus, thus representing the most common form of genetic reassortments that gives rise to a phenotypic change in the resultant strains.
With influenza, these changes are caused by influenza A viruses spread from birds and animals to humans, thereby creating new combinations of the HA and/or NA proteins on the surface of the virus. Such changes result in a new influenza A virus subtype. The appearance of a new influenza A virus subtype is the first step toward a pandemic. To cause a pandemic, however, the new virus subtype also would need the capacity to spread easily from person to person and be a subtype that is sufficiently dissimilar from the two typical strains (A and B) found in the human population. Once a new pandemic influenza virus emerges and spreads, it eventually becomes established and transmissible among human populations, circulating for many years as part of the seasonal epidemics of influenza.
While the extent and severity of a pandemic cannot be accurately predicted, several computer modeling studies suggest that the impact of a pandemic on the United States (and the world as a whole) could be substantial. In the absence of any control measures (e.g., vaccination or drugs), it has been estimated that a “medium-level” pandemic in the U.S. could cause 89,000 to 207,000 deaths, 314,000 to 734,000 hospitalizations, 18 to 42 million outpatient visits, and another 20 to 47 million incidents of illness. According to the Centers for Disease Control and Prevention (CDC), between 15% and 35% of the U.S. population could be affected by an influenza pandemic, with an economic impact estimated between approximately $70 and $170 billion. By summer 2009, CDC had reported more than 43,000 confined and probable cases of H1N1 in the U.S., with more than 300 of those resulting in death.
Biological organisms (also interchangeably referred to herein as “organisms” or “microorganisms”), such as bacteria and viruses, like influenza A, B, or a combination of organisms, and particularly pandemic influenza, threaten to quickly spread over large geographic ranges and through large populations, causing high rates of mortality and morbidity. Prior to mobilizing and implementing prevention tactics to ensure public health, it is critical to first and foremost detect and identify these organisms as soon as they appear. Early detection and surveillance to track the spread of such organisms might help mitigate the extensive damage predicted by the CDC in the event of a pandemic outbreak, e.g., influenza. Early detection is also expected to be critical in limiting or helping to treat the damage from any biological terrorism. Thus, a system to rapidly detect and identify organisms is most desirable.
Conventional techniques to detect and identify viruses, however, are not suitable for this task. Generally virus surveillance, detection and identification are time consuming (e.g., days to weeks, and in some cases, months), cumbersome to conduct, and have the potential of posing numerous health risks to health care personnel and even the general public. Most techniques typically require cold chain cultures (with safety level 3 to 4 protocols), which is associated with fairly high levels of risk. The conventional surveillance, detection, and identification process (collectively referred to herein as “the surveillance process”) typically includes culturing a live target specimen (interchangeably referred to herein as “targeted specimen,” “tissue,” or “sample”), such as bird, swine, human, or other living cells; transporting the sample to a suitable laboratory facility or other testing site, such as national, regional, or state testing laboratories; and then testing the target specimen for a range of biological organisms. Based on assays of genomic material (e.g. RNA and/or DNA) in the target sample, the organism(s) can often be identified.
Inherent in this identification and detection process is the need for bringing the target specimen back to a laboratory, thereby adding time and risk to the entire process. If the target specimen is found remotely, then it must be carefully transported to a suitable diagnostic laboratory so as to not harm, contaminate, or risk accidental exposure of the specimen—of the people handling the specimen during transport. During transportation, for example, the specimen is typically kept in a refrigerated or near frozen condition to ensure that the specimen is kept alive and the tissues to be tested remain intact.
Thus, Applicants have discovered a need in the art for a simple to use, stable, rapid diagnostic tool and product that, rather than culturing an organism and/or sending the specimen to a remote laboratory, would allow more rapid detection and identification of biological organisms, such as microorganisms (e.g., viruses and bacteria), at or adjacent a specimen collection site. The diagnostic tool should be portable and capable of being operated remotely from a conventional laboratory, and preferably would provide safety in such an environment compared to conventional diagnostic methods used in regional facilities, such as culturing such organisms.